The movie starts with a boy who belongs to prehistoric time hunting a fish, gets captured in a time vortex and reaches to the 20th century. In the 20th century, Nobita Nobi wants to run away from his home. As a result of failing to find an ideal home, Nobita decides to make a makeshift place to live. However, he still cannot find a place to live due to land property ownership laws. At the same time, Shizuka Minamoto, Takeshi "Gian" Goda, Suneo Honekawa and Doraemon want to run away from their homes. Nobita suggests that they should go back in time to live in a place with no human. The group agree with him and thus, they go to prehistoric Japan, 70,000 years in the past.
When they reach Japan, Doraemon assigns everyone a ministry. Shizuka is given the ministry of gardening, Gian gets the ministry of development, Suneo receives the ministry of landscape and Nobita receives the ministry of animals, with Doraemon overseeing all ministries. Nobita mixes the genes of different animal and creates a dragon, griffin and pegasus. When Doraemon comes, he hides them from him.
At night, the group eat the supper and decide to return home and visit there another day. On the next day, the boy from the start of the movie secretly moves into Nobita's room and hides inside the closet. When Gian and Suneo come, Gian fights with him and, due to weakness, the boy faints. On the arrival of Nobita, Shizuka and Doraemon, the group again moves to the past. They take the boy into their cave and when he regains consciousness, Shizuka gives him food. Meanwhile, Doraemon searches with a signal through time and learns that the boy hails from somewhere in present-day Nanjing, China, which has been already inhabited by humans since more than 70,000 years ago. Doraemon further uses a translation tool in order to understand him. He tells them that he belongs to the light tribe and his tribe got attacked by dark tribe who took all of his people. The group decide to help him.
They trace the dark tribe on Pegasus, Dragon and Griffin for four days. On the fourth day, they find and fight with them. However their shaman proves to be strong and gives them a strong challenge only to be defeated by Doraemon's gadgets. Unknown to them, the shaman possesses the power to restore. The group take the whole tribe to Japan to give them a peaceful place to live. At night, they return home.
Next day Doraemon tells everybody that the shaman can restore itself and the light tribe is still in danger, so they again go back in time. They arrive too late, as the dark tribe had already taken the light tribe. Again, the group trace the dark tribe with Doraemon's human train gadget, but Nobita gets lost and is separated from the group during a harsh snowstorm.
Except for Nobita, the rest of the group continue to move and they find the light tribe. Doraemon fights with Gigazombie, who is the king of spirits. Doraemon reveals him to be a time criminal who is creating his own world. He easily defeats Doraemon and the others.
On the other hand, Nobita finds a box near him and sees a hologram that tells him that if he needs help he should just press the button. Nobita's pet animals Pegasus, Dragon and Griffin return and they rescue his friend. However Gigazombie shuts them to a lone place. Nobita uses the button and the helper is revealed to be a time patrol who captures Gigazombie. At the end, Pegasus, Dragon and Griffin are taken to the future as they could not survive in the current era. The groups leaves for home.
